The laboratory of experimental complex systems (LECOS)

1) The theme school behaviour using the 5iD viewer instrument was further continued by

optimisation of the analytical software and man-made data analysis.

2) Using theAFM instrument (D. Malakhova) there were tested series of samples of

mesenchymal stem cells for the laboratory at Donau Universität Krems.

Fig. 1 Image of the mesenchymal stem cell using AFM at high resolution.

3) Nanoskopwas adopted by the Optax company and it is currently tested adopted version of

the software. The mesenchymal stem cells were also measured using nanoscope.

Fig. 2. Mesenchymal stem cell measured on nanoscope, LIL conversion.

4) In the field of the Belousov – Zhabotinsky we continued in the attempts to understand

properties of the model. We found that there are two distinct cases when states are defined

by natural numbers. The case when two neighbouring non-zero cells are needed for

evolution of cells the final ergodic state is a mixture of spirals and waves as they are

observed in the nature (see fig. 3). When just one non-zero cell is sufficient, the final state is

composed of filamentous structures. Spirals are restored in the presence of noise. There is

lower limit of noise for spiral formation. We believe that this observation explains the

frequent presence of spirals in nature. We offer also physico-chemical explanations for each

of the processes

Fig. 3. Comparison of the experiment and hodgepodge model for the case k1=k3=3. This is example

of the case when two neighbouring non-zero cells are needed for wave emanation.

Other activities:

Tomáš Náhlík, Renata Rychtáriková and Dalibor Štys lectured at the conference XIII Discussions in

Structural Molecular Biology, Anna Zhyrova presented a poster.

Article „ 5iD Viewer - Observation of Fish School Behaviour in Labyrinths and Use of Semantic and

Syntactic Entropy for School Structure Definition“was published in the electronic Waset Journal

In the connection to the IWWBIOconference in Granada were published article D. Štys, J. Urban, R.

Rychtáriková, A. Zhyrova a P. Císař Measurement in Biological Systems from the Self-organisation

Point of View andŠ. Papáček, J. Jablonský, C. Matonoha, R. Kaňa a S KindermannFRAP & FLIP: Two

sides of the same coin?. In Lecture Notes in Bioinformatics

http://link.springer.com/chapter/10.1007/978-3-319-16480-9_43, . Other article form this volume

were certainly reported by the LOSIP laboratory.

In the bookPrograms and Algorithms of Numerical Mathematics 17, ISBN 978-80-85823-64-6was

published article S. Papacek, J. Jablonský, CtiradMatonoha, On two methods for the parameter

estimation problem with spatio-temporal FRAP data

Article in the impacted journal is je Friederike Klemke, Antje Baier, Henning Knoop, Ramona Kern, Jiri

Jablonsky, Gabriele Beyer, Thomas Volkmer, Ralf Steuer, Wolfgang Lockau, Martin

Hagemann Identification of the light-independent phosphoserine pathway as additional source for

serine in the cyanobacterium Synechosystis sp. PCC 6803, Microbiology Papers in Press. Published

February 20, 2015 as doi:10.1099/mic.0.000055

Other articles were submitted.

Laboratory of Signal and Image Processing ( LoSIP )

The experiments with fish feeding monitoring system were held in cooperation with SINTEF

company and supported by AQUAEXCEL project. The recording of fish activity during feeding was

done in sea cage in Norway. The obtained experimental data will be analyzed and the results will be

used for optimization of fish feeding process.

The description and the results obtained from previously developed infrared reflection (IREF)

fish monitoring system for indoor tanks is currently prepared for publication in Aquacultural

Engineering journal. The article is planned to be submitted to the journal by the end of April 2015.

3D Fish Trajectory map using RGB-D images from Kinect

Steps have been taken till now:

1. RGB and Depth images from Kinect v1 has been collected with 1, 2, 3 and 4 fish. Images were

collected in Kinects near mode feature.

2. Real world X and Y coordinate have been determined using idTracker with acceptable accuracy

3. Depth images have been converted to point cloud for better processing, but, there was shifting

in Z value (the depth value) which makes it impossible for producing accurate trajectory.

4. Build-in aligning function in Kinect SDK has been used for aligning the RGB and Depth image,

although, the quality of RGB image was decreased, which may affect the quality of X and Y

coordinate determination using idTracker.

Comparison of experimental cell growth and logistic model

The amounts of individual cells (black curve) as well as the area (green) were compared with the

logistic model of population growth (red and blue respectively). The cells are occupying space

relatively according to their amount. The dead cells were automatically ignored in the algorithmically

evaluation (the movement stops).

Distributed knowledge database

The Biowes system is ready for use with new database hierarchy. The system will be incorporated

into Aquaexcel 2020 project, storing the Transnational access form (aims of the access, time

schedule, expected outputs). In BioWes is already implemented TNA form. It is possible to see the

evolution of project from proposal submission through experimental measurements to final results.

Everything is tracked via BioWes scientific data management. Users and project evaluators have

always possibility to see the progress of scientific work. In the end of project is possible to see the

whole experiment, from proposal submission to final results, included published paper.

Photographic chamber

The laboratory of signal and image processing started with development of photographic chamber

for fish skin colour evaluation. The chamber will provide standard light conditions, automatically

calibrate the white balance and colour response, estimate the size parameters of the fish, and

measure weight of the animal in single button solution.

The collaboration with the University of Vienna

The collaboration with the University of Vienna in the field of subtractive confocal fluorescence

microscopy imaging continues. We improved the pinhole signal gain acquisition and colour

transformation. The intermediate result offers the possibility to high resolved 3d structure of

chloroplasts and other organelles of selaginella serpens and peperomia metallica. The joint task will

continue in verification with immobilized cells during the z-stack measurements and comparison of

already known ultra structure (there is no OTF etalons for fluorescence).

Left: optimal setting 1AU, right subtractive image.

The laboratory of tissue culture

The head of the laboratory of tissue culture represented activities of the laboratory in

international conference „Invasive aquatic species of animals“in České Budějovice. The

international conference was held on December 9th, 2014. The theme „Toxicity study of

extracts from animal and plant tissue on animal cells in vitro, by time-lapse

cinephotomicrography “ interested listeners in the conference thanks processed slides with

practical demonstration video with direct contact animal cells and tested samples. The

presented theme was inserted in collection, which was issued for this international

conference.

The article “Interaction of metal alloys and cell lines” was published. The article wrote Ing.

Homolkova in cooperation with Ing. Březina. The article appeared in the second issue of

the impact magazine Chemické listy 109, 151-154(2015).

Workshop Povrchy 2015

The team of the laboratory of tissue culture organized the second workshop named „ The based

time-lapse cinephotomicrography“. The workshop held from February 25 to March 3,2015.Working

meeting was intended for researchers who use or want to use the method of "live cell imaging"

which is a progressive method to research the interactions of living cells in vitro with other materials

or tissues. The workshop was selective with 8 can didates from Technické univerzity v Liberci, Fakulty

textilní, Katedry netkaných textilií a nanovlákenných materiálů. The content of the theory test

tolerance bio surfaces and their practical implementation. Three-dimensional substrates. Method of

colonization, including statistics. A lot of experiments was done on their ported materials in various

technological ways e.g. PCL (micro and nanofibres) and PLA (micro and nanofibres).The experiments

and active cooperation was very beneficial for all parties. The laboratory of tissue culture will

continue to work with those workplaces.